Schema for R-Loop DRIP-Seq (S2) - R-Loop DRIP-Seq in S2 Cells

Database: dm6 Primary Table: CSE99014_dH1_RNH1_untreated_peakzilla Row Count: 26,508 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5436	`int(10) unsigned`	range
`chromEnd`	5730	`int(10) unsigned`	range
`name`	peakzilla_18508	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.88	`float`	range
`pValue`	-1	`float`	range
`qValue`	1.62342	`float`	range
`peak`	147	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5436	5730	peakzilla_18508	2	.	2.88	-1	1.62342	147
585	chr2L	5746	6040	peakzilla_2171	6	.	4.62	-1	2.38722	147
585	chr2L	9853	10147	peakzilla_16418	3	.	5.3	-1	1.72354	147
585	chr2L	16847	17141	peakzilla_14881	3	.	4.28	-1	1.77469	147
585	chr2L	19677	19971	peakzilla_10269	3	.	6.39	-1	1.93181	147
585	chr2L	47270	47564	peakzilla_17796	2	.	2.19	-1	1.65758	147
585	chr2L	102483	102777	peakzilla_17577	2	.	3.17	-1	1.67162	147
585	chr2L	116449	116743	peakzilla_19456	2	.	3.62	-1	1.57512	147
585	chr2L	123355	123649	peakzilla_17742	2	.	3.02	-1	1.66555	147
586	chr2L	132283	132577	peakzilla_15625	3	.	2.97	-1	1.74232	147

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

R-Loop DRIP-Seq (S2) (rloopDRIPSeq) Track Description


	Description These tracks show the putative locations of R-loops based on DRIP-Seq data from Drosophila melanogaster S2 Cells. The samples that were treated with RNase H served as additional controls for identifying R-loops. The regions that are enriched in the DRIP-Seq reads were identified by MACS2 and Peakzilla. The log likelihood ratio evidence tracks were produced by MACS2. The Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05. The DRIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the accession number GSE99014. References Bayona-Feliu A, Casas-Lamesa A, Reina O, Bernués J, Azorin F. Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin. Nat Commun. 2017 Aug 18;8(1):283. Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Description